Can't tell you why this is happening but I can tell you that for consistency reasons I use the Sony Library software to transfer every book to my reader so I don't use DE to transfer downloaded books to my reader.
When I download a book from DE it puts the file in the "My Digital Editions" folder. I then open up the Sony Library software and transfer the book file to my Sony by dragging it from Windows Explorer into the library software. Perhaps the same would work if Calibre was used instead of the Sony software.
This doesn't resolve your problem but it's worth a try as a workaround.
Cheers,
Terry.
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